In 1991-1993 we amended a DNA-protein recognition model advanced in 1975 [Mol. Biol. (Engl. trans.) 25, 819-836 (1991), J. Biomol. Struct. Dynam. 10, 763-784 (1993)]. Here we test our assumptions with a specially designed tripeptide L-Thr-L-Val-L-Thr-NH-NH-Dns (Dns is 5-dimethylaminonaphthalene-1-sulfonic acid residue). It is shown to dimerize in solution (as evidenced by the nonlinear concentration dependence of its fluorescence) and to bind with DNA mainly in β-dimeric form (S-shaped adsorption isotherm obtained by equilibrium dialysis). The tripeptide is bound in the DNA minor groove (whence it can be displaced with distamycin A), and such complexes become able to associate into ?biduplex? structures (nonlinear dependence of the linear dichroism of bound peptide on DNA concentration). The peptide dimers clearly prefer the AT pairs [half-saturating peptide concentrations are (0.6-0.7)·10^-4 M for poly(dA)·poly(dT) but exceed (2.5-2.8)·10^-4 M for poly(dG)·poly(dC)]. These results agree nicely with our earlier suggestions. Since Dns-tagged trivaline has been shown [Cold Spring Harbor Symp. Quant. Biol. 47, 361-372 (1983)] to prefer the GC pairs, we think it now becomes possible to design oligopeptides that would specifically bind to any predefined nucleotide sequence.

Key words: Threonine; Tripeptide; β-dimer; and Protein-DNA recognition.